A multi-scale three-dimensional variational (MS-3DVAR) scheme is developed to assimilate high-resolution Himawari-8 sea surface temperature (SST) data for the first time into an operational ocean nowcast/forecast system targeting the North Western Pacific, JCOPE2. MS-3DVAR improves representation of the Kuroshio path south of Japan, its associated sea level variations, and temperature/salinity profiles south of Japan, the Kuroshio/Oyashio mixed water region, and the Japan Sea as compared to those of the products by the traditional single-scale 3DVAR. Validation results demonstrate that MS-3DVAR well assimilates the sparsely distributed in situ temperature and salinity profiles data by spreading the information over the large scale and by representing the detailed information near the measurement points. MS-3DVAR succeeds to assimilate the Himawari-8 SST product without noisy features caused by the cloud effects. We also find that MS-3DVAR is more effective for estimating oceanic conditions in regions with smaller mesoscale variability including the mixed water region and Japan Sea than in south of Japan.